Cytochromes P-450 2C11 and 2C13 are the major CYPs in rat liver microsomes. Despite a high degree of sequence identity, these two isozymes display different positional and regio-specific metabolism of steroid hormones, such as testosterone. CYP2C11 converts testosterone to 2alpha-hydroxyl and 16alpha-hydroxyl metabolites, while CYP2C13 produces primarily the 6beta-hydroxyl metabolite. Using a human CYP2C9 crystal structure as the template, homology models were generated for CYP2C11 and CYP2C13. Despite similar volume of the binding pockets for CYP2C11 and CYP2C13, the models for these two CYPs showed a substantial difference in the shape of the substrate-binding sites. Substrate docking using rigid and induced-fit methods showed that testosterone fits into the substrate-binding sites of both CYP2C11 and CYP2C13 without the need of added constraints. These docking exercises appear to support testosterone binding in both CYP2C11 and CYP2C13. A constrained docking using energy minimization is required to position testosterone for more precise positional and regio-specificity in supporting the observed metabolism. These results demonstrate the complexity of using modeling for understanding the binding of substrate to CYPs, and suggest that, as a complement to the metabolism data, modeling and docking may yield reliable structural information for the molecular interaction between the substrate and the CYPs.